User: Adaikalavan Ramasamy

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Posts by Adaikalavan Ramasamy

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Comment: C: Merging microarray datasets
... Kathy, this depends on two thing. 1) how similar are the chip types? For example, hgu95a and hgu95av2, two Affymetrix chips which differed by one probeset. I do not know why it differed by one probeset but I suppose one just omitted the extra probeset and preprocess them together. 2) the type of ...
written 9.6 years ago by Adaikalavan Ramasamy1.8k
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Answer: A: calculating median expression between to identical gene names in data frame
... I am assuming that you want to "average" the gene profiles. See if this works: colMedians <- function(mat) apply(mat, 2, median) sapply( split( df, gids ), colMedians ) This is computationally inefficient as the number of rows increase but this should be reasonably fast for 180 rows. ...
written 9.7 years ago by Adaikalavan Ramasamy1.8k
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Comment: C: Cox Model
... That's a good idea as you can address the sample selection bias. You might also be interested in reading the following papers if you haven't done so already (there are other on a similar topic): Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random valida ...
written 9.8 years ago by Adaikalavan Ramasamy1.8k
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Comment: C: Cox Model
... Eleni, Note that some of the genes that declared as significant in a univariate analysis could be highly correlated. Thus, some of the selected genes would not be informative in building the multivariate model. You might want to consider reducing the dimensionality by first grouping the genes into ...
written 9.8 years ago by Adaikalavan Ramasamy1.8k
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Comment: C: warning message in KS test
... Can you find just ONE instance (i.e. one gene) that shows this behaviour and email us the dput() on that vector please. It is very hard to understand what you have shown us without an example. Thank you. Regards, Adai James Anderson wrote: > Francois, > > What I wanted to do is to sele ...
written 10.1 years ago by Adaikalavan Ramasamy1.8k
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[OT] compatible preprocessing for Affy and non-Affy
... [[Apologies in advance since this may be an off topic subject but I have tried hard without finding any consensus.]] Problem: I am trying to combine data from Affymetrix platform and non-Affymetrix platform (most of them two-color technologies) from the raw data (e.g. CEL, GPR). Therefore I need to ...
normalization preprocessing affy written 10.5 years ago by Adaikalavan Ramasamy1.8k
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Comment: C: Error in RankProd package
... James is correct. You could also try justRMA() in a fresh R session, preferably with minimal number of other programmes running in the background. Or ask a friend/collaborator who has access to a machine with more RAM or buy more RAM. Regards, Adai James W. MacDonald wrote: > Hi Gunther, > ...
written 10.7 years ago by Adaikalavan Ramasamy1.8k
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Comment: C: urgent..
... I may have seen CEL files being saved as .xls, .csv, .txt as well. The easiest thing is to ask how many .csv files there are. If there are one .csv file per array, then can you post the first 30 lines or so. It might just be a case of renaming the files. Regards, Adai On Mon, 2006-04-17 at 08:5 ...
written 11.6 years ago by Adaikalavan Ramasamy1.8k
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Answer: A: Predicting number of replicates
... Err, what are your objectives here ? Is it to do sample size calculations or simply wanting to have data to publish it. On Wed, 2006-04-12 at 17:14 -0400, Khan, Sohail wrote: > Dear List, > > I have a basic statistical question regarding a Microarray data set. However, I am not an statis ...
written 11.6 years ago by Adaikalavan Ramasamy1.8k
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Answer: A: A questions related to affymetrix chip normalization from multiple platform
... How many samples do you have with HGU133A, HGU133B and HGU133 plus 2.0 ? You might have to preprocess the 3 different chip types separately and then merge using union approach. This means that the samples from A and B chip type would have missing values. MAS 5.0 is outdated and has been shown to p ...
written 11.6 years ago by Adaikalavan Ramasamy1.8k

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